## File: SRSet-class.Rd

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 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687 \name{SRSet-class} \docType{class} \alias{SRSet-class} \alias{readCount} \alias{readData} \alias{readIndex} \alias{sourcePath} \alias{phenoData,SRSet-method} \alias{experimentPath,SRSet-method} \alias{show,SRSet-method} \alias{detail,SRSet-method} \title{(Legacy) A base class for Roche experiment-wide data} \description{ This class coordinates phenotype (sample) and sequence data, primarily as used on the Roche platform. Conceptually, this class has reads from a single experiment represented as a long vector, ordered by sample. The \code{readCount} slot indicates the number of reads in each sample, so that the sum of \code{readCount} is the total number of reads in the experiment. The \code{readIndex} field is a light-weight indicator of which reads from all those available that are currently referenced by the \code{SRSet}. } \section{Objects from the Class}{ Objects of this class are not usually created directly, but instead are created by a derived class, e.g., \code{\linkS4class{RocheSet}}. } \section{Slots}{ \describe{ \item{\code{sourcePath}:}{Object of class \code{"ExperimentPath"}, containing the directory path where sequence files can be found.} \item{\code{readIndex}:}{Object of class \code{"integer"} indicating specific sequences included in the experiment.} \item{\code{readCount}:}{Object of class \code{"integer"} containing the number of reads in each sample included in the experiment. The sum of this vector is the total number of reads.} \item{\code{phenoData}:}{Object of class \code{"AnnotatedDataFrame"} describing each sample in the experiment. The number of rows of \code{phenoData} equals the number of elements in \code{readCount}.} \item{\code{readData}:}{Object of class \code{"AnnotatedDataFrame"} containing annotations on all reads.} } } \section{Extends}{ Class \code{"\linkS4class{.ShortReadBase}"}, directly. } \section{Methods}{ \describe{ \item{experimentPath}{\code{signature(object = "SRSet")}: return the \code{\linkS4class{ExperimentPath}} associated with this object.} \item{phenoData}{\code{signature(object = "SRSet")}: return the \code{\linkS4class{phenoData}} associated with this object.} \item{readCount}{\code{signature(object="SRSet")}:} \item{readIndex}{\code{signature(object="SRSet")}:} \item{readData}{\code{signature(object="SRSet")}:} \item{sourcePath}{\code{signature(object="SRSet")}: Retrieve the corresponding slot from \code{object}.} \item{show}{\code{signature(object = "SRSet")}: display the contents of this object.} \item{detail}{\code{signature(x = "SRSet")}: provide more extensive information on the object.} } } \author{Michael Lawrence } \examples{ showClass("SRSet") } \keyword{classes}